Only because Peach/luigi/etc are playable.
Obviously if we didn''t have peach and bowser they would be beyond popular for smash. Everyone else wouldn't even get a mention. (even then paper peach and E gadd absolutely are not popular choices)
Its unfathomable because it isnt that way; yes, characters in mario do have a slight edge in iconography- but a lot of the iconic Pokemon (the original starters) are some of the ones counted out.
There are core characters in the Pokemon universe that are not merely popular, such as Pokemon trainer. Much more capable than any captured Damsel, canonically, as well.
What if Fire Emblem were represented by Michaiah, Anna, and Black Knight?
What if Star Fox only had Krystal, Falco, and Andross?
What if Animal Crossing were Tom Nook, Cherry, and KK Slider?
What if Ice Climbers only had the Polar Bear?